/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.JvSwingUtils;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.AbstractCellEditor;
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
/**
- * DOCUMENT ME!
+ * Base class for the Preferences panel.
*
* @author $author$
* @version $Revision$
*/
public class GPreferences extends JPanel
{
- JTabbedPane tabbedPane = new JTabbedPane();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel okCancelPanel = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
- protected JCheckBox quality = new JCheckBox();
-
- JPanel visualTab = new JPanel();
-
- JPanel visual2Tab = new JPanel();
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
+ false, true);
+ /*
+ * Visual tab components
+ */
protected JCheckBox fullScreen = new JCheckBox();
- protected JCheckBox conservation = new JCheckBox();
+ protected JCheckBox openoverv = new JCheckBox();
- protected JCheckBox identity = new JCheckBox();
+ protected JCheckBox seqLimit = new JCheckBox();
- protected JCheckBox annotations = new JCheckBox();
+ protected JCheckBox rightAlign = new JCheckBox();
- protected JPanel minColour = new JPanel();
+ protected JComboBox<String> fontSizeCB = new JComboBox<String>();
- JLabel mincolourLabel = new JLabel();
+ protected JComboBox<String> fontStyleCB = new JComboBox<String>();
- protected JPanel maxColour = new JPanel();
+ protected JComboBox<String> fontNameCB = new JComboBox<String>();
- JLabel maxcolourLabel = new JLabel();
+ protected JCheckBox showOccupancy = new JCheckBox();
- JLabel gapLabel = new JLabel();
+ protected JCheckBox showUnconserved = new JCheckBox();
+
+ protected JCheckBox idItalics = new JCheckBox();
- protected JComboBox colour = new JComboBox();
+ protected JCheckBox smoothFont = new JCheckBox();
- JLabel colourLabel = new JLabel();
+ protected JCheckBox scaleProteinToCdna = new JCheckBox();
- JLabel fontLabel = new JLabel();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
- protected JComboBox fontSizeCB = new JComboBox();
+ protected JCheckBox wrap = new JCheckBox();
- protected JComboBox fontStyleCB = new JComboBox();
+ protected JComboBox<String> sortby = new JComboBox<String>();
- protected JComboBox fontNameCB = new JComboBox();
+ protected JComboBox<String> sortAnnBy = new JComboBox<String>();
- protected JComboBox gapSymbolCB = new JComboBox();
+ protected JComboBox<String> sortAutocalc = new JComboBox<String>();
protected JCheckBox startupCheckbox = new JCheckBox();
protected JTextField startupFileTextfield = new JTextField();
- JPanel connectTab = new JPanel();
+ // below are in the 'second column'
+ protected JCheckBox annotations = new JCheckBox();
- JLabel serverLabel = new JLabel();
+ protected JCheckBox quality = new JCheckBox();
- protected JList linkURLList = new JList();
+ protected JCheckBox conservation = new JCheckBox();
- protected JTextField proxyServerTB = new JTextField();
+ protected JCheckBox identity = new JCheckBox();
- protected JTextField proxyPortTB = new JTextField();
+ protected JCheckBox showGroupConsensus = new JCheckBox();
- JLabel portLabel = new JLabel();
+ protected JCheckBox showGroupConservation = new JCheckBox();
- JLabel browserLabel = new JLabel();
+ protected JCheckBox showConsensHistogram = new JCheckBox();
- protected JTextField defaultBrowser = new JTextField();
+ protected JCheckBox showConsensLogo = new JCheckBox();
- JButton newLink = new JButton();
+ protected JCheckBox showDbRefTooltip = new JCheckBox();
- JButton editLink = new JButton();
+ protected JCheckBox showNpTooltip = new JCheckBox();
- JButton deleteLink = new JButton();
+ /*
+ * Structure tab and components
+ */
+ protected JPanel structureTab;
- JScrollPane linkScrollPane = new JScrollPane();
+ protected JCheckBox structFromPdb = new JCheckBox();
- JPanel linkPanel = new JPanel();
+ protected JCheckBox useRnaView = new JCheckBox();
- BorderLayout borderLayout2 = new BorderLayout();
+ protected JCheckBox addSecondaryStructure = new JCheckBox();
- JPanel editLinkButtons = new JPanel();
+ protected JCheckBox addTempFactor = new JCheckBox();
- GridLayout gridLayout1 = new GridLayout();
+ protected JComboBox<String> structViewer = new JComboBox<String>();
- protected JList linkNameList = new JList();
+ protected JTextField chimeraPath = new JTextField();
- JPanel linkPanel2 = new JPanel();
+ protected ButtonGroup mappingMethod = new ButtonGroup();
- BorderLayout borderLayout3 = new BorderLayout();
+ protected JRadioButton siftsMapping = new JRadioButton();
- protected JCheckBox useProxy = new JCheckBox();
+ protected JRadioButton nwMapping = new JRadioButton();
- JPanel jPanel1 = new JPanel();
+ /*
+ * Colours tab components
+ */
+ protected JPanel minColour = new JPanel();
- TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
+ protected JPanel maxColour = new JPanel();
- TitledBorder titledBorder2 = new TitledBorder("File Output");
+ protected JComboBox<String> protColour = new JComboBox<String>();
- GridBagLayout gridBagLayout2 = new GridBagLayout();
+ protected JComboBox<String> nucColour = new JComboBox<String>();
- GridBagLayout gridBagLayout1 = new GridBagLayout();
+ /*
+ * Connections tab components
+ */
+ protected JTable linkUrlTable = new JTable();
- GridBagLayout gridBagLayout3 = new GridBagLayout();
+ protected JButton editLink = new JButton();
- protected JComboBox sortby = new JComboBox();
+ protected JButton deleteLink = new JButton();
- JLabel sortLabel = new JLabel();
+ protected JTextField filterTB = new JTextField();
- JPanel jPanel2 = new JPanel();
+ protected JButton doReset = new JButton();
- JPanel visual2panel = new JPanel();
+ protected JButton userOnly = new JButton();
- GridLayout gridLayout2 = new GridLayout();
+ protected JLabel portLabel = new JLabel();
- GridLayout gridLayout4 = new GridLayout();
+ protected JLabel serverLabel = new JLabel();
- JPanel annsettingsPanel = new JPanel();
+ protected JTextField proxyServerTB = new JTextField();
- JPanel autoAnnotSettings1 = new JPanel();
+ protected JTextField proxyPortTB = new JTextField();
- JPanel autoAnnotSettings2 = new JPanel();
+ protected JTextField defaultBrowser = new JTextField();
- JPanel autoAnnotSettings3 = new JPanel();
+ protected JCheckBox useProxy = new JCheckBox();
- JPanel exportTab = new JPanel();
+ protected JCheckBox usagestats = new JCheckBox();
- JLabel epsLabel = new JLabel();
+ protected JCheckBox questionnaire = new JCheckBox();
+
+ protected JCheckBox versioncheck = new JCheckBox();
- protected JComboBox epsRendering = new JComboBox();
+ /*
+ * Output tab components
+ */
+ protected JComboBox<Object> epsRendering = new JComboBox<Object>();
protected JLabel userIdWidthlabel = new JLabel();
protected JTextField userIdWidth = new JTextField();
- JLabel jLabel1 = new JLabel();
-
protected JCheckBox blcjv = new JCheckBox();
protected JCheckBox pileupjv = new JCheckBox();
protected JCheckBox pfamjv = new JCheckBox();
- FlowLayout flowLayout1 = new FlowLayout();
-
protected JCheckBox pirjv = new JCheckBox();
- JPanel jPanel11 = new JPanel();
+ protected JCheckBox modellerOutput = new JCheckBox();
- Font verdana11 = JvSwingUtils.getLabelFont();
+ protected JCheckBox embbedBioJSON = new JCheckBox();
- protected JCheckBox seqLimit = new JCheckBox();
+ /*
+ * Editing tab components
+ */
+ protected JCheckBox autoCalculateConsCheck = new JCheckBox();
- GridLayout gridLayout3 = new GridLayout();
+ protected JCheckBox padGaps = new JCheckBox();
- protected JCheckBox smoothFont = new JCheckBox();
+ protected JCheckBox sortByTree = new JCheckBox();
- JPanel calcTab = new JPanel();
+ /*
+ * DAS Settings tab
+ */
+ protected JPanel dasTab = new JPanel();
- protected JCheckBox autoCalculateConsCheck = new JCheckBox();
+ /*
+ * Web Services tab
+ */
+ protected JPanel wsTab = new JPanel();
- protected JCheckBox padGaps = new JCheckBox();
+ /**
+ * Creates a new GPreferences object.
+ */
+ public GPreferences()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
- protected JCheckBox modellerOutput = new JCheckBox();
+ /**
+ * Construct the panel and its tabbed sub-panels.
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ final JTabbedPane tabbedPane = new JTabbedPane();
+ this.setLayout(new BorderLayout());
+ JPanel okCancelPanel = initOkCancelPanel();
+ this.add(tabbedPane, BorderLayout.CENTER);
+ this.add(okCancelPanel, BorderLayout.SOUTH);
+
+ tabbedPane.add(initVisualTab(),
+ MessageManager.getString("label.visual"));
+
+ tabbedPane.add(initColoursTab(),
+ MessageManager.getString("label.colours"));
+
+ tabbedPane.add(initStructureTab(),
+ MessageManager.getString("label.structure"));
+
+ tabbedPane.add(initConnectionsTab(),
+ MessageManager.getString("label.connections"));
+
+ tabbedPane.add(initLinksTab(),
+ MessageManager.getString("label.urllinks"));
+
+ tabbedPane.add(initOutputTab(),
+ MessageManager.getString("label.output"));
+
+ tabbedPane.add(initEditingTab(),
+ MessageManager.getString("label.editing"));
+
+ /*
+ * See DasSourceBrowser for the real work of configuring this tab.
+ */
+ dasTab.setLayout(new BorderLayout());
+ tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
+
+ /*
+ * See WsPreferences for the real work of configuring this tab.
+ */
+ wsTab.setLayout(new BorderLayout());
+ tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+
+ /*
+ * Handler to validate a tab before leaving it - currently only for
+ * Structure.
+ */
+ tabbedPane.addChangeListener(new ChangeListener()
+ {
+ private Component lastTab;
- protected JPanel dasPanel = new JPanel();
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ if (lastTab == structureTab
+ && tabbedPane.getSelectedComponent() != structureTab)
+ {
+ if (!validateStructure())
+ {
+ tabbedPane.setSelectedComponent(structureTab);
+ return;
+ }
+ }
+ lastTab = tabbedPane.getSelectedComponent();
+ }
- BorderLayout borderLayout4 = new BorderLayout();
+ });
+ }
- protected JPanel wsPanel = new JPanel();
+ /**
+ * Initialises the Editing tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initEditingTab()
+ {
+ JPanel editingTab = new JPanel();
+ editingTab.setLayout(null);
+ autoCalculateConsCheck.setFont(LABEL_FONT);
+ autoCalculateConsCheck.setText(MessageManager
+ .getString("label.autocalculate_consensus"));
+ autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+ padGaps.setFont(LABEL_FONT);
+ padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
+ padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+ sortByTree.setFont(LABEL_FONT);
+ sortByTree
+ .setText(MessageManager.getString("label.sort_with_new_tree"));
+ sortByTree
+ .setToolTipText(MessageManager
+ .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+ sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+ editingTab.add(autoCalculateConsCheck);
+ editingTab.add(padGaps);
+ editingTab.add(sortByTree);
+ return editingTab;
+ }
- BorderLayout borderLayout5 = new BorderLayout();
+ /**
+ * Initialises the Output tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOutputTab()
+ {
+ JPanel outputTab = new JPanel();
+ outputTab.setLayout(null);
+ JLabel epsLabel = new JLabel();
+ epsLabel.setFont(LABEL_FONT);
+ epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
+ epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+ epsRendering.setFont(LABEL_FONT);
+ epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+ JLabel jLabel1 = new JLabel();
+ jLabel1.setFont(LABEL_FONT);
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText(MessageManager.getString("label.append_start_end"));
+ jLabel1.setFont(LABEL_FONT);
+ fastajv.setFont(LABEL_FONT);
+ fastajv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setText(MessageManager.getString("label.clustal") + " ");
+ blcjv.setText(MessageManager.getString("label.blc") + " ");
+ fastajv.setText(MessageManager.getString("label.fasta") + " ");
+ msfjv.setText(MessageManager.getString("label.msf") + " ");
+ pfamjv.setText(MessageManager.getString("label.pfam") + " ");
+ pileupjv.setText(MessageManager.getString("label.pileup") + " ");
+ msfjv.setFont(LABEL_FONT);
+ msfjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setText(MessageManager.getString("label.pir") + " ");
+ JPanel jPanel11 = new JPanel();
+ jPanel11.setFont(LABEL_FONT);
+ TitledBorder titledBorder2 = new TitledBorder(
+ MessageManager.getString("label.file_output"));
+ jPanel11.setBorder(titledBorder2);
+ jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+ GridLayout gridLayout3 = new GridLayout();
+ jPanel11.setLayout(gridLayout3);
+ gridLayout3.setRows(8);
+ blcjv.setFont(LABEL_FONT);
+ blcjv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setFont(LABEL_FONT);
+ clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
+ pfamjv.setFont(LABEL_FONT);
+ pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pileupjv.setFont(LABEL_FONT);
+ pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setFont(LABEL_FONT);
+ pirjv.setHorizontalAlignment(SwingConstants.LEFT);
+ autoIdWidth.setFont(LABEL_FONT);
+ autoIdWidth.setText(MessageManager
+ .getString("label.automatically_set_id_width"));
+ autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager
+ .getString("label.adjusts_width_generated_eps_png")));
+ autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
+ autoIdWidth.addActionListener(new ActionListener()
+ {
- protected JCheckBox wrap = new JCheckBox();
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ autoIdWidth_actionPerformed();
+ }
+ });
+ userIdWidthlabel.setFont(LABEL_FONT);
+ userIdWidthlabel.setText(MessageManager
+ .getString("label.figure_id_column_width"));
+ userIdWidth
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
+ userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
+ userIdWidth.setText("");
+ userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+ userIdWidth.addActionListener(new ActionListener()
+ {
- protected JCheckBox rightAlign = new JCheckBox();
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ userIdWidth_actionPerformed();
+ }
+ });
+ modellerOutput.setFont(LABEL_FONT);
+ modellerOutput.setText(MessageManager
+ .getString("label.use_modeller_output"));
+ modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ embbedBioJSON.setFont(LABEL_FONT);
+ embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
+ embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
- protected JCheckBox showUnconserved = new JCheckBox();
+ jPanel11.add(jLabel1);
+ jPanel11.add(blcjv);
+ jPanel11.add(clustaljv);
+ jPanel11.add(fastajv);
+ jPanel11.add(msfjv);
+ jPanel11.add(pfamjv);
+ jPanel11.add(pileupjv);
+ jPanel11.add(pirjv);
+ outputTab.add(autoIdWidth);
+ outputTab.add(userIdWidth);
+ outputTab.add(userIdWidthlabel);
+ outputTab.add(modellerOutput);
+ outputTab.add(embbedBioJSON);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(jPanel11);
+ return outputTab;
+ }
- protected JCheckBox showDbRefTooltip = new JCheckBox();
+ /**
+ * Initialises the Connections tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initConnectionsTab()
+ {
+ JPanel connectTab = new JPanel();
+ connectTab.setLayout(new GridBagLayout());
- protected JCheckBox showNpTooltip = new JCheckBox();
+ // Label for browser text box
+ JLabel browserLabel = new JLabel();
+ browserLabel.setFont(LABEL_FONT);
+ browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
+ browserLabel.setText(MessageManager
+ .getString("label.default_browser_unix"));
+ defaultBrowser.setFont(LABEL_FONT);
+ defaultBrowser.setText("");
- protected JCheckBox idItalics = new JCheckBox();
+ defaultBrowser.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ defaultBrowser_mouseClicked(e);
+ }
+ }
+ });
- protected JCheckBox openoverv = new JCheckBox();
+ JPanel proxyPanel = initConnTabProxyPanel();
+ initConnTabCheckboxes();
- protected JCheckBox usagestats = new JCheckBox();
+ // Add default Browser text box
+ connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(10, 0, 5, 5), 5, 1));
+ defaultBrowser.setFont(LABEL_FONT);
+ defaultBrowser.setText("");
- protected JCheckBox questionnaire = new JCheckBox();
+ connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
+ 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+ new Insets(10, 0, 5, 10), 30, 1));
- protected JCheckBox versioncheck = new JCheckBox();
+ // Add proxy server panel
+ connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
+ GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+ new Insets(10, 0, 5, 12), 4, 10));
- protected JLabel showGroupbits = new JLabel();
+ // Add usage stats, version check and questionnaire checkboxes
+ connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
+ connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 10), 70, 1));
+ connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
- protected JLabel showConsensbits = new JLabel();
+ // Add padding so the panel doesn't look ridiculous
+ JPanel spacePanel = new JPanel();
+ connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0,
+ 0, 0, 5), 70, 1));
- protected JCheckBox showConsensLogo = new JCheckBox();
+ return connectTab;
+ }
- protected JCheckBox showConsensHistogram = new JCheckBox();
+ /**
+ * Initialises the Links tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initLinksTab()
+ {
+ JPanel linkTab = new JPanel();
+ linkTab.setLayout(new GridBagLayout());
+
+ // Set up table for Url links
+ linkUrlTable.setFillsViewportHeight(true);
+ linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
+ linkUrlTable.setAutoCreateRowSorter(true);
+ linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ // adjust row height so radio buttons actually fit
+ // don't do this in the renderer, it causes the awt thread to activate
+ // constantly
+ JRadioButton temp = new JRadioButton();
+ linkUrlTable.setRowHeight(temp.getMinimumSize().height);
+
+ // Table in scrollpane so that the table is given a scrollbar
+ JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
+ linkScrollPane.setBorder(null);
- protected JCheckBox showGroupConsensus = new JCheckBox();
+ // Panel for links functionality
+ JPanel linkPanel = new JPanel(new GridBagLayout());
+ linkPanel.setBorder(new TitledBorder(MessageManager
+ .getString("label.url_linkfrom_sequence_id")));
+
+ // Put the Url links panel together
+
+ // Buttons go at top right, resizing only resizes the blank space vertically
+ JPanel buttonPanel = initLinkTabUrlButtons();
+ GridBagConstraints linkConstraints1 = new GridBagConstraints();
+ linkConstraints1.insets = new Insets(0, 0, 5, 0);
+ linkConstraints1.gridx = 0;
+ linkConstraints1.gridy = 0;
+ linkConstraints1.weightx = 1.0;
+ linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
+ linkTab.add(buttonPanel, linkConstraints1);
+
+ // Links table goes at top left, resizing resizes the table
+ GridBagConstraints linkConstraints2 = new GridBagConstraints();
+ linkConstraints2.insets = new Insets(0, 0, 5, 5);
+ linkConstraints2.gridx = 0;
+ linkConstraints2.gridy = 1;
+ linkConstraints2.weightx = 1.0;
+ linkConstraints2.weighty = 1.0;
+ linkConstraints2.fill = GridBagConstraints.BOTH;
+ linkTab.add(linkScrollPane, linkConstraints2);
+
+ // Filter box and buttons goes at bottom left, resizing resizes the text box
+ JPanel filterPanel = initLinkTabFilterPanel();
+ GridBagConstraints linkConstraints3 = new GridBagConstraints();
+ linkConstraints3.insets = new Insets(0, 0, 0, 5);
+ linkConstraints3.gridx = 0;
+ linkConstraints3.gridy = 2;
+ linkConstraints3.weightx = 1.0;
+ linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
+ linkTab.add(filterPanel, linkConstraints3);
+
+ return linkTab;
+ }
- protected JCheckBox showGroupConservation = new JCheckBox();
+ private JPanel initLinkTabFilterPanel()
+ {
+ // Filter textbox and reset button
+ JLabel filterLabel = new JLabel(
+ MessageManager.getString("label.filter"));
+ filterLabel.setFont(LABEL_FONT);
+ filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ filterTB.setFont(LABEL_FONT);
+ filterTB.setText("");
+
+ doReset.setText(MessageManager.getString("action.showall"));
+ userOnly.setText(MessageManager.getString("action.customfilter"));
+
+ // Panel for filter functionality
+ JPanel filterPanel = new JPanel(new GridBagLayout());
+ filterPanel.setBorder(new TitledBorder("Filter"));
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+
+ filterPanel.add(filterLabel, gbc);
+
+ GridBagConstraints gbc1 = new GridBagConstraints();
+ gbc1.gridx = 1;
+ gbc1.gridwidth = 2;
+ gbc1.fill = GridBagConstraints.HORIZONTAL;
+ gbc1.anchor = GridBagConstraints.WEST;
+ gbc1.weightx = 1.0;
+ filterPanel.add(filterTB, gbc1);
+
+ GridBagConstraints gbc2 = new GridBagConstraints();
+ gbc2.gridx = 3;
+ gbc2.fill = GridBagConstraints.NONE;
+ gbc2.anchor = GridBagConstraints.WEST;
+ filterPanel.add(doReset, gbc2);
+
+ GridBagConstraints gbc3 = new GridBagConstraints();
+ gbc3.gridx = 4;
+ gbc3.fill = GridBagConstraints.NONE;
+ gbc3.anchor = GridBagConstraints.WEST;
+ filterPanel.add(userOnly, gbc3);
+
+ return filterPanel;
+ }
+
+ private JPanel initLinkTabUrlButtons()
+ {
+ // Buttons for new / edit / delete Url links
+ JButton newLink = new JButton();
+ newLink.setText(MessageManager.getString("action.new"));
- protected JCheckBox shareSelections = new JCheckBox();
+ editLink.setText(MessageManager.getString("action.edit"));
- protected JCheckBox followHighlight = new JCheckBox();
+ deleteLink.setText(MessageManager.getString("action.delete"));
- protected JCheckBox sortByTree = new JCheckBox();
+ // no current selection, so initially disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
+
+ newLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newLink_actionPerformed(e);
+ }
+ });
+
+ editLink.setText(MessageManager.getString("action.edit"));
+ editLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ editLink_actionPerformed(e);
+ }
+ });
+
+ deleteLink.setText(MessageManager.getString("action.delete"));
+ deleteLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteLink_actionPerformed(e);
+ }
+ });
+
+ JPanel buttonPanel = new JPanel(new GridBagLayout());
+ buttonPanel.setBorder(new TitledBorder("Edit links"));
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ buttonPanel.add(newLink, gbc);
+
+ GridBagConstraints gbc1 = new GridBagConstraints();
+ gbc1.gridx = 1;
+ gbc1.gridy = 0;
+ gbc1.fill = GridBagConstraints.NONE;
+ buttonPanel.add(editLink, gbc1);
+
+ GridBagConstraints gbc2 = new GridBagConstraints();
+ gbc2.gridx = 2;
+ gbc2.gridy = 0;
+ gbc2.fill = GridBagConstraints.NONE;
+ buttonPanel.add(deleteLink, gbc2);
+
+ GridBagConstraints gbc3 = new GridBagConstraints();
+ gbc3.gridx = 3;
+ gbc3.gridy = 0;
+ gbc3.fill = GridBagConstraints.HORIZONTAL;
+ gbc3.weightx = 1.0;
+ JPanel spacePanel = new JPanel();
+ spacePanel.setBorder(null);
+ buttonPanel.add(spacePanel, gbc3);
+
+ return buttonPanel;
+ }
/**
- * Creates a new GPreferences object.
+ * Initialises the proxy server panel in the Connections tab
+ *
+ * @return the proxy server panel
*/
- public GPreferences()
+ private JPanel initConnTabProxyPanel()
{
- try
- {
- jbInit();
- } catch (Exception ex)
+ // Label for server text box
+ serverLabel.setText(MessageManager.getString("label.address"));
+ serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ serverLabel.setFont(LABEL_FONT);
+
+ // Proxy server and port text boxes
+ proxyServerTB.setFont(LABEL_FONT);
+ proxyPortTB.setFont(LABEL_FONT);
+
+ // Label for Port text box
+ portLabel.setFont(LABEL_FONT);
+ portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ portLabel.setText(MessageManager.getString("label.port"));
+
+ // Use proxy server checkbox
+ useProxy.setFont(LABEL_FONT);
+ useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
+ useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
+ useProxy.setText(MessageManager.getString("label.use_proxy_server"));
+ useProxy.addActionListener(new ActionListener()
{
- ex.printStackTrace();
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ useProxy_actionPerformed();
+ }
+ });
+
+ // Make proxy server panel
+ JPanel proxyPanel = new JPanel();
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.proxy_server"));
+ proxyPanel.setBorder(titledBorder1);
+ proxyPanel.setLayout(new GridBagLayout());
+ proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 2, 0), 5, 0));
+ proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 0, 2, 0), 11, 0));
+ proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 2, 5, 185), 2, -4));
+ proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 2), 54, 1));
+ proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 0), 263, 1));
+
+ return proxyPanel;
}
/**
- * DOCUMENT ME!
+ * Initialises the checkboxes in the Connections tab
+ */
+ private void initConnTabCheckboxes()
+ {
+ // Usage stats checkbox label
+ usagestats.setText(MessageManager
+ .getString("label.send_usage_statistics"));
+ usagestats.setFont(LABEL_FONT);
+ usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
+ usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Questionnaire checkbox label
+ questionnaire.setText(MessageManager
+ .getString("label.check_for_questionnaires"));
+ questionnaire.setFont(LABEL_FONT);
+ questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
+ questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Check for latest version checkbox label
+ versioncheck.setText(MessageManager
+ .getString("label.check_for_latest_version"));
+ versioncheck.setFont(LABEL_FONT);
+ versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
+ versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
+ }
+
+ /**
+ * Initialises the parent panel which contains the tabbed sections.
*
- * @throws Exception
- * DOCUMENT ME!
+ * @return
*/
- private void jbInit() throws Exception
+ private JPanel initOkCancelPanel()
{
- this.setLayout(borderLayout1);
- ok.setText("OK");
+ JButton ok = new JButton();
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
}
});
- cancel.setText("Cancel");
+ JButton cancel = new JButton();
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
}
});
+ JPanel okCancelPanel = new JPanel();
+ okCancelPanel.add(ok);
+ okCancelPanel.add(cancel);
+ return okCancelPanel;
+ }
+
+ /**
+ * Initialises the Colours tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initColoursTab()
+ {
+ JPanel coloursTab = new JPanel();
+ coloursTab.setBorder(new TitledBorder(MessageManager
+ .getString("action.open_new_alignment")));
+ coloursTab.setLayout(new FlowLayout());
+ JLabel mincolourLabel = new JLabel();
+ mincolourLabel.setFont(LABEL_FONT);
+ mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ mincolourLabel.setText(MessageManager.getString("label.min_colour"));
+ minColour.setFont(LABEL_FONT);
+ minColour.setBorder(BorderFactory.createEtchedBorder());
+ minColour.setPreferredSize(new Dimension(40, 20));
+ minColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ minColour_actionPerformed(minColour);
+ }
+ });
+ JLabel maxcolourLabel = new JLabel();
+ maxcolourLabel.setFont(LABEL_FONT);
+ maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
+ maxColour.setFont(LABEL_FONT);
+ maxColour.setBorder(BorderFactory.createEtchedBorder());
+ maxColour.setPreferredSize(new Dimension(40, 20));
+ maxColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ maxColour_actionPerformed(maxColour);
+ }
+ });
+
+ protColour.setFont(LABEL_FONT);
+ protColour.setBounds(new Rectangle(172, 225, 155, 21));
+ JLabel protColourLabel = new JLabel();
+ protColourLabel.setFont(LABEL_FONT);
+ protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ protColourLabel.setText(MessageManager
+ .getString("label.prot_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab, MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ protColourLabel, protColour);
+
+ nucColour.setFont(LABEL_FONT);
+ nucColour.setBounds(new Rectangle(172, 240, 155, 21));
+ JLabel nucColourLabel = new JLabel();
+ nucColourLabel.setFont(LABEL_FONT);
+ nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ nucColourLabel.setText(MessageManager
+ .getString("label.nuc_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab, MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ nucColourLabel, nucColour);
+
+ JPanel annotationShding = new JPanel();
+ annotationShding.setBorder(new TitledBorder(MessageManager
+ .getString("label.annotation_shading_default")));
+ annotationShding.setLayout(new GridLayout(1, 2));
+ JvSwingUtils.addtoLayout(annotationShding, MessageManager
+ .getString("label.default_minimum_colour_annotation_shading"),
+ mincolourLabel, minColour);
+ JvSwingUtils.addtoLayout(annotationShding, MessageManager
+ .getString("label.default_maximum_colour_annotation_shading"),
+ maxcolourLabel, maxColour);
+ coloursTab.add(annotationShding); // , FlowLayout.LEFT);
+ return coloursTab;
+ }
+
+ /**
+ * Initialises the Structure tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initStructureTab()
+ {
+ structureTab = new JPanel();
+
+ structureTab.setBorder(new TitledBorder(MessageManager
+ .getString("label.structure_options")));
+ structureTab.setLayout(null);
+ final int width = 400;
+ final int height = 22;
+ final int lineSpacing = 25;
+ int ypos = 15;
+
+ structFromPdb.setFont(LABEL_FONT);
+ structFromPdb
+ .setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
+ structFromPdb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean selected = structFromPdb.isSelected();
+ // enable other options only when the first is checked
+ useRnaView.setEnabled(selected);
+ addSecondaryStructure.setEnabled(selected);
+ addTempFactor.setEnabled(selected);
+ }
+ });
+ structureTab.add(structFromPdb);
+
+ // indent checkboxes that are conditional on the first one
+ ypos += lineSpacing;
+ useRnaView.setFont(LABEL_FONT);
+ useRnaView.setText(MessageManager.getString("label.use_rnaview"));
+ useRnaView.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(useRnaView);
+
+ ypos += lineSpacing;
+ addSecondaryStructure.setFont(LABEL_FONT);
+ addSecondaryStructure.setText(MessageManager
+ .getString("label.autoadd_secstr"));
+ addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addSecondaryStructure);
+
+ ypos += lineSpacing;
+ addTempFactor.setFont(LABEL_FONT);
+ addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
+ addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addTempFactor);
+
+ ypos += lineSpacing;
+ JLabel viewerLabel = new JLabel();
+ viewerLabel.setFont(LABEL_FONT);
+ viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
+ viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
+ structureTab.add(viewerLabel);
+
+ structViewer.setFont(LABEL_FONT);
+ structViewer.setBounds(new Rectangle(160, ypos, 120, height));
+ structViewer.addItem(ViewerType.JMOL.name());
+ structViewer.addItem(ViewerType.CHIMERA.name());
+ structViewer.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ structureViewer_actionPerformed((String) structViewer
+ .getSelectedItem());
+ }
+ });
+ structureTab.add(structViewer);
+
+ ypos += lineSpacing;
+ JLabel pathLabel = new JLabel();
+ pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+ pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ pathLabel.setText(MessageManager.getString("label.chimera_path"));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ pathLabel.setToolTipText(tooltip);
+ pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
+ structureTab.add(pathLabel);
+
+ chimeraPath.setFont(LABEL_FONT);
+ chimeraPath.setText("");
+ chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
+ chimeraPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser();
+ if (chosen != null)
+ {
+ chimeraPath.setText(chosen);
+ }
+ }
+ }
+ });
+ structureTab.add(chimeraPath);
+
+ ypos += lineSpacing;
+ nwMapping.setFont(LABEL_FONT);
+ nwMapping.setText(MessageManager.getString("label.nw_mapping"));
+ siftsMapping.setFont(LABEL_FONT);
+ siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
+ mappingMethod.add(nwMapping);
+ mappingMethod.add(siftsMapping);
+ JPanel mappingPanel = new JPanel();
+ mappingPanel.setFont(LABEL_FONT);
+ TitledBorder mmTitledBorder = new TitledBorder(
+ MessageManager.getString("label.mapping_method"));
+ mmTitledBorder.setTitleFont(LABEL_FONT);
+ mappingPanel.setBorder(mmTitledBorder);
+ mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
+ // GridLayout mappingLayout = new GridLayout();
+ mappingPanel.setLayout(new GridLayout());
+ mappingPanel.add(nwMapping);
+ mappingPanel.add(siftsMapping);
+ structureTab.add(mappingPanel);
+
+ ypos += lineSpacing;
+ ypos += lineSpacing;
+ FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
+ PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
+ docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
+ structureTab.add(docFieldPref);
+
+ return structureTab;
+ }
+
+ /**
+ * Action on choosing a structure viewer from combobox options.
+ *
+ * @param selectedItem
+ */
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ }
+
+ /**
+ * Show a dialog for the user to choose a file. Returns the chosen path, or
+ * null on Cancel.
+ *
+ * @return
+ */
+ protected String openFileChooser()
+ {
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+
+ // chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ /**
+ * Validate the structure tab preferences; if invalid, set focus on this tab.
+ *
+ * @param e
+ */
+ protected boolean validateStructure(FocusEvent e)
+ {
+ if (!validateStructure())
+ {
+ e.getComponent().requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ protected boolean validateStructure()
+ {
+ return false;
+ }
+
+ /**
+ * Initialises the Visual tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initVisualTab()
+ {
+ JPanel visualTab = new JPanel();
+ visualTab.setBorder(new TitledBorder(MessageManager
+ .getString("action.open_new_alignment")));
+ visualTab.setLayout(null);
+ fullScreen.setFont(LABEL_FONT);
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+ fullScreen.setText(MessageManager.getString("label.maximize_window"));
quality.setEnabled(false);
- quality.setFont(verdana11);
+ quality.setFont(LABEL_FONT);
quality.setHorizontalAlignment(SwingConstants.RIGHT);
quality.setHorizontalTextPosition(SwingConstants.LEFT);
quality.setSelected(true);
- quality.setText("Quality");
- visualTab.setBorder(new TitledBorder("Open new alignment"));
- visualTab.setLayout(null);
- visual2Tab.setBorder(new TitledBorder("Open new alignment"));
- visual2Tab.setLayout(new FlowLayout());
- fullScreen.setFont(verdana11);
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
- fullScreen.setText("Maximise Window");
+ quality.setText(MessageManager.getString("label.quality"));
conservation.setEnabled(false);
- conservation.setFont(verdana11);
+ conservation.setFont(LABEL_FONT);
conservation.setHorizontalAlignment(SwingConstants.RIGHT);
conservation.setHorizontalTextPosition(SwingConstants.LEFT);
conservation.setSelected(true);
- conservation.setText("Conservation");
+ conservation.setText(MessageManager.getString("label.conservation"));
identity.setEnabled(false);
- identity.setFont(verdana11);
+ identity.setFont(LABEL_FONT);
identity.setHorizontalAlignment(SwingConstants.RIGHT);
identity.setHorizontalTextPosition(SwingConstants.LEFT);
identity.setSelected(true);
- identity.setText("Consensus");
- showGroupbits.setFont(verdana11);
+ identity.setText(MessageManager.getString("label.consensus"));
+ showOccupancy.setFont(LABEL_FONT);
+ showOccupancy.setEnabled(false);
+ showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
+ showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
+ showOccupancy.setSelected(true);
+ showOccupancy.setText(MessageManager.getString("label.occupancy"));
+
+ JLabel showGroupbits = new JLabel();
+ showGroupbits.setFont(LABEL_FONT);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText("Show group:");
- showConsensbits.setFont(verdana11);
+ showGroupbits.setText(MessageManager.getString("action.show_group")
+ + ":");
+ JLabel showConsensbits = new JLabel();
+ showConsensbits.setFont(LABEL_FONT);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText("Consensus:");
+ showConsensbits.setText(MessageManager.getString("label.consensus")
+ + ":");
showConsensHistogram.setEnabled(false);
- showConsensHistogram.setFont(verdana11);
+ showConsensHistogram.setFont(LABEL_FONT);
showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
- showConsensHistogram.setText("Histogram");
+ showConsensHistogram.setText(MessageManager
+ .getString("label.histogram"));
showConsensLogo.setEnabled(false);
- showConsensLogo.setFont(verdana11);
+ showConsensLogo.setFont(LABEL_FONT);
showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensLogo.setSelected(true);
- showConsensLogo.setText("Logo");
+ showConsensLogo.setText(MessageManager.getString("label.logo"));
showGroupConsensus.setEnabled(false);
- showGroupConsensus.setFont(verdana11);
+ showGroupConsensus.setFont(LABEL_FONT);
showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConsensus.setSelected(true);
- showGroupConsensus.setText("Consensus");
+ showGroupConsensus.setText(MessageManager.getString("label.consensus"));
showGroupConservation.setEnabled(false);
- showGroupConservation.setFont(verdana11);
+ showGroupConservation.setFont(LABEL_FONT);
showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
- showGroupConservation.setText("Conservation");
+ showGroupConservation.setText(MessageManager
+ .getString("label.conservation"));
showNpTooltip.setEnabled(true);
- showNpTooltip.setFont(verdana11);
+ showNpTooltip.setFont(LABEL_FONT);
showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showNpTooltip.setSelected(true);
- showNpTooltip.setText("Non-positional Features");
+ showNpTooltip.setText(MessageManager
+ .getString("label.non_positional_features"));
showDbRefTooltip.setEnabled(true);
- showDbRefTooltip.setFont(verdana11);
+ showDbRefTooltip.setFont(LABEL_FONT);
showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText("Database References");
- annotations.setFont(verdana11);
+ showDbRefTooltip.setText(MessageManager
+ .getString("label.database_references"));
+ annotations.setFont(LABEL_FONT);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEADING);
+ annotations.setHorizontalTextPosition(SwingConstants.LEFT);
annotations.setSelected(true);
- annotations.setText("Show Annotations");
- annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.setText(MessageManager.getString("label.show_annotations"));
+ // annotations.setBounds(new Rectangle(169, 12, 200, 23));
annotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
});
identity.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
});
showGroupConsensus.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
}
});
- showUnconserved.setFont(verdana11);
+ showUnconserved.setFont(LABEL_FONT);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setSelected(true);
- showUnconserved.setText("Show Unconserved");
+ showUnconserved.setText(MessageManager
+ .getString("action.show_unconserved"));
showUnconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showunconserved_actionPerformed(e);
}
});
- // / TODO: fit these in to preferences panel!!!!!
- shareSelections.setFont(verdana11);
- shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
- shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
- shareSelections.setSelected(true);
- shareSelections.setText("Share selection across views");
- followHighlight.setFont(verdana11);
- followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
- followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
- // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
- followHighlight.setSelected(true);
- followHighlight.setText("Scroll to highlighted regions");
-
- gapLabel.setFont(verdana11);
+
+ // TODO these are not yet added to / action from Preferences
+ // JCheckBox shareSelections = new JCheckBox();
+ // shareSelections.setFont(verdana11);
+ // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+ // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+ // shareSelections.setSelected(true);
+ // shareSelections.setText(MessageManager
+ // .getString("label.share_selection_across_views"));
+ // JCheckBox followHighlight = new JCheckBox();
+ // followHighlight.setFont(verdana11);
+ // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ // followHighlight.setSelected(true);
+ // followHighlight.setText(MessageManager
+ // .getString("label.scroll_highlighted_regions"));
+
+ seqLimit.setFont(LABEL_FONT);
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+ seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+ seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
+ smoothFont.setFont(LABEL_FONT);
+ smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+ smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+ smoothFont.setText(MessageManager.getString("label.smooth_font"));
+ scaleProteinToCdna.setFont(LABEL_FONT);
+ scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
+ scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
+ scaleProteinToCdna.setText(MessageManager
+ .getString("label.scale_protein_to_cdna"));
+ scaleProteinToCdna.setToolTipText(MessageManager
+ .getString("label.scale_protein_to_cdna_tip"));
+ JLabel gapLabel = new JLabel();
+ gapLabel.setFont(LABEL_FONT);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- gapLabel.setText("Gap Symbol ");
- colour.setFont(verdana11);
- colour.setBounds(new Rectangle(172, 225, 155, 21));
- colourLabel.setFont(verdana11);
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText("Alignment Colour ");
- fontLabel.setFont(verdana11);
+ gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
+ JLabel fontLabel = new JLabel();
+ fontLabel.setFont(LABEL_FONT);
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- fontLabel.setText("Font ");
- fontSizeCB.setFont(verdana11);
- fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
- fontStyleCB.setFont(verdana11);
- fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
- fontNameCB.setFont(verdana11);
- fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
- gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
- mincolourLabel.setFont(verdana11);
- mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- mincolourLabel.setText("Minimum Colour");
- minColour.setFont(verdana11);
- minColour.setBorder(BorderFactory.createEtchedBorder());
- minColour.setPreferredSize(new Dimension(40, 20));
- minColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- minColour_actionPerformed();
- }
- });
- maxcolourLabel.setFont(verdana11);
- maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- maxcolourLabel.setText("Maximum Colour ");
- maxColour.setFont(verdana11);
- maxColour.setBorder(BorderFactory.createEtchedBorder());
- maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- maxColour_actionPerformed();
- }
- });
+ fontLabel.setText(MessageManager.getString("label.font"));
+ fontSizeCB.setFont(LABEL_FONT);
+ fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
+ fontStyleCB.setFont(LABEL_FONT);
+ fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
+ fontNameCB.setFont(LABEL_FONT);
+ fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
+ gapSymbolCB.setFont(LABEL_FONT);
+ gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+ gapSymbolCB.setRenderer(dlcr);
- startupCheckbox.setText("Open file");
- startupCheckbox.setFont(verdana11);
+ startupCheckbox.setText(MessageManager.getString("action.open_file"));
+ startupCheckbox.setFont(LABEL_FONT);
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
startupCheckbox.setSelected(true);
- startupFileTextfield.setFont(verdana11);
- startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
+ startupFileTextfield.setFont(LABEL_FONT);
+ startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
startupFileTextfield.addMouseListener(new MouseAdapter()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() > 1)
}
});
- connectTab.setLayout(gridBagLayout3);
- serverLabel.setText("Address");
- serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- serverLabel.setFont(verdana11);
- proxyServerTB.setFont(verdana11);
- proxyPortTB.setFont(verdana11);
- portLabel.setFont(verdana11);
- portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- portLabel.setText("Port");
- browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
- browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText("Default Browser (Unix)");
- defaultBrowser.setFont(verdana11);
- defaultBrowser.setText("");
- usagestats.setText("Send usage statistics");
- usagestats.setFont(verdana11);
- usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
- usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
- questionnaire.setText("Check for questionnaires");
- questionnaire.setFont(verdana11);
- questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
- questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
- versioncheck.setText("Check for latest version");
- versioncheck.setFont(verdana11);
- versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
- versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
- newLink.setText("New");
- newLink.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- newLink_actionPerformed(e);
- }
- });
- editLink.setText("Edit");
- editLink.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- editLink_actionPerformed(e);
- }
- });
- deleteLink.setText("Delete");
- deleteLink.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- deleteLink_actionPerformed(e);
- }
- });
-
- linkURLList.addListSelectionListener(new ListSelectionListener()
- {
- public void valueChanged(ListSelectionEvent e)
- {
- int index = linkURLList.getSelectedIndex();
- linkNameList.setSelectedIndex(index);
- }
- });
-
- linkNameList.addListSelectionListener(new ListSelectionListener()
- {
- public void valueChanged(ListSelectionEvent e)
- {
- int index = linkNameList.getSelectedIndex();
- linkURLList.setSelectedIndex(index);
- }
- });
-
- linkScrollPane.setBorder(null);
- linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
- linkPanel.setLayout(borderLayout2);
- editLinkButtons.setLayout(gridLayout1);
- gridLayout1.setRows(3);
- linkNameList.setFont(verdana11);
- linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- linkPanel2.setLayout(borderLayout3);
- linkURLList.setFont(verdana11);
- linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
- defaultBrowser.addMouseListener(new MouseAdapter()
- {
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- defaultBrowser_mouseClicked(e);
- }
- }
- });
- useProxy.setFont(verdana11);
- useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
- useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
- useProxy.setText("Use a proxy server");
- useProxy.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- useProxy_actionPerformed();
- }
- });
- jPanel1.setBorder(titledBorder1);
- jPanel1.setLayout(gridBagLayout1);
- sortby.setFont(verdana11);
- sortby.setBounds(new Rectangle(172, 249, 155, 21));
- sortLabel.setFont(verdana11);
+ sortby.setFont(LABEL_FONT);
+ sortby.setBounds(new Rectangle(172, 260, 155, 21));
+ JLabel sortLabel = new JLabel();
+ sortLabel.setFont(LABEL_FONT);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- sortLabel.setText("Sort by ");
- jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
- jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(12);
- exportTab.setLayout(null);
- epsLabel.setFont(verdana11);
- epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText("EPS Rendering Style");
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
- epsRendering.setFont(verdana11);
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
- jLabel1.setFont(verdana11);
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText("Append /start-end (/15-380)");
- jLabel1.setFont(verdana11);
- fastajv.setFont(verdana11);
- fastajv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setText("Clustal ");
- blcjv.setText("BLC ");
- fastajv.setText("Fasta ");
- msfjv.setText("MSF ");
- pfamjv.setText("PFAM ");
- pileupjv.setText("Pileup ");
- msfjv.setFont(verdana11);
- msfjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setText("PIR ");
- jPanel11.setFont(verdana11);
- jPanel11.setBorder(titledBorder2);
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
- jPanel11.setLayout(gridLayout3);
- blcjv.setFont(verdana11);
- blcjv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setFont(verdana11);
- clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
- pfamjv.setFont(verdana11);
- pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
- pileupjv.setFont(verdana11);
- pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setFont(verdana11);
- pirjv.setHorizontalAlignment(SwingConstants.LEFT);
- seqLimit.setFont(verdana11);
- seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
- seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
- seqLimit.setText("Full Sequence Id");
- gridLayout3.setRows(8);
- smoothFont.setFont(verdana11);
- smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
- smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
- smoothFont.setText("Smooth Font");
- calcTab.setLayout(null);
- autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
- autoCalculateConsCheck.setText("AutoCalculate Consensus");
- autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(JvSwingUtils.getLabelFont());
- padGaps.setText("Pad Gaps When Editing");
- padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- sortByTree.setFont(JvSwingUtils.getLabelFont());
- sortByTree.setText("Sort With New Tree");
- sortByTree
- .setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
- sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
-
- autoIdWidth.setFont(JvSwingUtils.getLabelFont());
- autoIdWidth.setText("Automatically set ID width");
- autoIdWidth
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")
- + "</html>");
- autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
- autoIdWidth.addActionListener(new ActionListener()
- {
+ sortLabel.setText(MessageManager.getString("label.sort_by"));
+ sortAnnBy.setFont(LABEL_FONT);
+ sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
+ JLabel sortAnnLabel = new JLabel();
+ sortAnnLabel.setFont(LABEL_FONT);
+ sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
+ sortAutocalc.setFont(LABEL_FONT);
+ sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
+
+ JPanel annsettingsPanel = new JPanel();
+ annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
+ annsettingsPanel.setBorder(new EtchedBorder());
+ visualTab.add(annsettingsPanel);
+ Border jb = new EmptyBorder(1, 1, 4, 5);
+ annotations.setBorder(jb);
+ showOccupancy.setBorder(jb);
+ quality.setBorder(jb);
+ conservation.setBorder(jb);
+ identity.setBorder(jb);
+ showConsensbits.setBorder(jb);
+ showGroupbits.setBorder(jb);
+ showGroupConsensus.setBorder(jb);
+ showGroupConservation.setBorder(jb);
+ showConsensHistogram.setBorder(jb);
+ showConsensLogo.setBorder(jb);
- @Override
- public void actionPerformed(ActionEvent e)
- {
- autoIdWidth_actionPerformed();
- }
- });
- userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
- userIdWidthlabel.setText("Figure ID column width");
- userIdWidth
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
- + "</html>");
- userIdWidthlabel
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
- + "</html>");
- userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
- userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
- userIdWidth.setText("");
- userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
- userIdWidth.addActionListener(new ActionListener()
- {
+ JPanel autoAnnotSettings = new JPanel();
+ annsettingsPanel.add(autoAnnotSettings);
+ autoAnnotSettings.setLayout(new GridLayout(0, 2));
+ autoAnnotSettings.add(annotations);
+ autoAnnotSettings.add(quality);
+ // second row of autoannotation box
+ autoAnnotSettings = new JPanel();
+ annsettingsPanel.add(autoAnnotSettings);
+
+ autoAnnotSettings.setLayout(new GridLayout(0, 3));
+ autoAnnotSettings.add(conservation);
+ autoAnnotSettings.add(identity);
+ autoAnnotSettings.add(showOccupancy);
+ autoAnnotSettings.add(showGroupbits);
+ autoAnnotSettings.add(showGroupConservation);
+ autoAnnotSettings.add(showGroupConsensus);
+ autoAnnotSettings.add(showConsensbits);
+ autoAnnotSettings.add(showConsensHistogram);
+ autoAnnotSettings.add(showConsensLogo);
+
+
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userIdWidth_actionPerformed();
- }
- });
- modellerOutput.setFont(JvSwingUtils.getLabelFont());
- modellerOutput.setText("Use Modeller Output");
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ JPanel tooltipSettings = new JPanel();
+ tooltipSettings.setBorder(new TitledBorder(MessageManager
+ .getString("label.sequence_id_tooltip")));
+ tooltipSettings.setBounds(173, 140, 220, 62);
+ tooltipSettings.setLayout(new GridLayout(2, 1));
+ tooltipSettings.add(showDbRefTooltip);
+ tooltipSettings.add(showNpTooltip);
+ visualTab.add(tooltipSettings);
- dasPanel.setLayout(borderLayout4);
- wsPanel.setLayout(borderLayout5);
- wrap.setFont(JvSwingUtils.getLabelFont());
+ wrap.setFont(LABEL_FONT);
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
- wrap.setText("Wrap Alignment");
- rightAlign.setFont(JvSwingUtils.getLabelFont());
+ wrap.setText(MessageManager.getString("label.wrap_alignment"));
+ rightAlign.setFont(LABEL_FONT);
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
- rightAlign.setText("Right Align Ids");
- idItalics.setFont(JvSwingUtils.getLabelFont());
+ rightAlign.setText(MessageManager.getString("label.right_align_ids"));
+ idItalics.setFont(LABEL_FONT_ITALIC);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText("Sequence Name Italics");
- openoverv.setFont(JvSwingUtils.getLabelFont());
- openoverv.setActionCommand("Open Overview");
+ idItalics.setText(MessageManager
+ .getString("label.sequence_name_italics"));
+ openoverv.setFont(LABEL_FONT);
+ openoverv.setActionCommand(MessageManager
+ .getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
- openoverv.setText("Open Overview");
+ openoverv.setText(MessageManager.getString("label.open_overview"));
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
+ jPanel2.setLayout(new GridLayout(14, 1));
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(showUnconserved);
jPanel2.add(idItalics);
jPanel2.add(smoothFont);
+ jPanel2.add(scaleProteinToCdna);
jPanel2.add(gapLabel);
jPanel2.add(wrap);
jPanel2.add(sortLabel);
+ jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);
- visualTab.add(annotations);
+ visualTab.add(jPanel2);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
+ visualTab.add(sortAnnBy);
+ visualTab.add(sortAutocalc);
visualTab.add(gapSymbolCB);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
- annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
- annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
- annsettingsPanel.add(autoAnnotSettings1);
- annsettingsPanel.add(autoAnnotSettings2);
- annsettingsPanel.add(autoAnnotSettings3);
- autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
- visualTab.add(annsettingsPanel);
- Border jb = new EmptyBorder(1, 1, 4, 5);
- quality.setBorder(jb);
- conservation.setBorder(jb);
- identity.setBorder(jb);
- showConsensbits.setBorder(jb);
- showGroupbits.setBorder(jb);
- showGroupConsensus.setBorder(jb);
- showGroupConservation.setBorder(jb);
- showConsensHistogram.setBorder(jb);
- showConsensLogo.setBorder(jb);
-
- autoAnnotSettings2.add(conservation);
- autoAnnotSettings1.add(quality);
- autoAnnotSettings3.add(identity);
- autoAnnotSettings1.add(showGroupbits);
- autoAnnotSettings3.add(showGroupConsensus);
- autoAnnotSettings2.add(showGroupConservation);
- autoAnnotSettings1.add(showConsensbits);
- autoAnnotSettings2.add(showConsensHistogram);
- autoAnnotSettings3.add(showConsensLogo);
-
- JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
- tooltipSettings.setBounds(173, 130, 200, 62);
- tooltipSettings.setLayout(new GridLayout(2, 1));
- tooltipSettings.add(showDbRefTooltip);
- tooltipSettings.add(showNpTooltip);
- visualTab.add(tooltipSettings);
- visualTab.add(jPanel2);
- JvSwingUtils.addtoLayout(visual2Tab,
- "Default Colourscheme for alignment", colourLabel, colour);
- JPanel annotationShding = new JPanel();
- annotationShding.setBorder(new TitledBorder(
- "Annotation Shading Default"));
- annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding,
- "Default Minimum Colour for annotation shading",
- mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding,
- "Default Maximum Colour for annotation shading",
- maxcolourLabel, maxColour);
- visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
-
- // visual2panel.add(minColour);
- // visual2panel.add(maxColour);
- // visual2Tab.add(visual2panel);
-
- linkPanel.add(editLinkButtons, BorderLayout.EAST);
- editLinkButtons.add(newLink, null);
- editLinkButtons.add(editLink, null);
- editLinkButtons.add(deleteLink, null);
- linkPanel.add(linkScrollPane, BorderLayout.CENTER);
- linkScrollPane.getViewport().add(linkPanel2, null);
- linkPanel2.add(linkURLList, BorderLayout.CENTER);
- linkPanel2.add(linkNameList, BorderLayout.WEST);
- okCancelPanel.add(ok);
- okCancelPanel.add(cancel);
- this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-
- this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
- jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 4, 0), 5, 0));
- jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 0, 4, 0), 11, 6));
- connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 16, 0, 0, 12), 359, -17));
- connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 21, 0, 35, 12), 4, 6));
- connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(16, 0, 0, 0), 5, 1));
- jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 54, 1));
- jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 0), 263, 1));
- connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(15, 0, 0, 15), 307, 1));
- connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
-
- jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 5, 185), 2, -4));
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
- gapSymbolCB.setRenderer(dlcr);
-
- tabbedPane.add(visualTab, "Visual");
- tabbedPane.add(visual2Tab, "Colours");
- tabbedPane.add(connectTab, "Connections");
- tabbedPane.add(exportTab, "Output");
- jPanel11.add(jLabel1);
- jPanel11.add(blcjv);
- jPanel11.add(clustaljv);
- jPanel11.add(fastajv);
- jPanel11.add(msfjv);
- jPanel11.add(pfamjv);
- jPanel11.add(pileupjv);
- jPanel11.add(pirjv);
- exportTab.add(autoIdWidth);
- exportTab.add(userIdWidth);
- exportTab.add(userIdWidthlabel);
- exportTab.add(modellerOutput);
- tabbedPane.add(calcTab, "Editing");
- calcTab.add(autoCalculateConsCheck);
- calcTab.add(padGaps);
- calcTab.add(sortByTree);
-
- tabbedPane.add(dasPanel, "DAS Settings");
- tabbedPane.add(wsPanel, "Web Services");
-
- exportTab.add(epsLabel);
- exportTab.add(epsRendering);
- exportTab.add(jPanel11);
+ return visualTab;
}
protected void autoIdWidth_actionPerformed()
}
- protected void maxColour_actionPerformed()
+ protected void maxColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
-
}
- protected void minColour_actionPerformed()
+ protected void minColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
-
}
protected void showunconserved_actionPerformed(ActionEvent e)
public void useProxy_actionPerformed()
{
- proxyServerTB.setEnabled(useProxy.isSelected());
- proxyPortTB.setEnabled(useProxy.isSelected());
+ boolean enabled = useProxy.isSelected();
+ portLabel.setEnabled(enabled);
+ serverLabel.setEnabled(enabled);
+ proxyServerTB.setEnabled(enabled);
+ proxyPortTB.setEnabled(enabled);
+ }
+
+ /**
+ * Customer renderer for JTable: supports column of radio buttons
+ */
+ public class RadioButtonRenderer extends JRadioButton implements
+ TableCellRenderer
+ {
+ public RadioButtonRenderer()
+ {
+ setHorizontalAlignment(CENTER);
+ setToolTipText(MessageManager.getString("label.urltooltip"));
+ }
+
+ @Override
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus, int row,
+ int column)
+ {
+ setSelected((boolean) value);
+
+ // set colours to match rest of table
+ if (isSelected)
+ {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
+ }
+ return this;
+ }
}
+ /**
+ * Customer cell editor for JTable: supports column of radio buttons in
+ * conjunction with renderer
+ */
+ public class RadioButtonEditor extends AbstractCellEditor implements
+ TableCellEditor
+ {
+ private JRadioButton button = new JRadioButton();
+
+ public RadioButtonEditor()
+ {
+ button.setHorizontalAlignment(SwingConstants.CENTER);
+ this.button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fireEditingStopped();
+ }
+ });
+ }
+
+ @Override
+ public Component getTableCellEditorComponent(JTable table,
+ Object value, boolean isSelected, int row, int column)
+ {
+ button.setSelected((boolean) value);
+ return button;
+ }
+
+ @Override
+ public Object getCellEditorValue()
+ {
+ return button.isSelected();
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff